Coming back to this, maybe Hendrik could chime in on when MC goes to the Cover Art\Series or \Seasons folders?
I used to "trick" MC to get the right Cover Art by assigning S01E01 the Series Cover Art, and S02E01 the Season 2 Cover Art and so on.
In the screen shot below, you can see that works for Orange/Black, Portlandia, Always Sunny, Entourage, and Lucky Louie. For Californication, since I don't have Season 1, it seems to work as well (first Episode I have is S02E01 so it uses Season 2 Cover Art). For Weeds, since I only have random Episodes, the trick does not work (all the Episodes I have just have screen shot Episode Cover Art assigned).
Worse though, for The League and Eastbound and Down, it doesn't work at all; despite having S01E01 assigned the Series Cover Art it just shows some random Episode's screen shot Cover Art.
In the second screen shot, you can see that if I drill down into the Series child level, it still doesn't show the Series Cover Art.
I have the same problem with my New and Unwatched Library Items. It only works correctly if the Library Item starts with Series as the parent level. Is it possible to have MC go to the Cover Art directory for Series and Season each time they come up, regardless of what level they are in the Library Item/View?